Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-4-Internal Loop pdb1s1iF3.n1662-1691
Source: [PDB-id:chain] 1s1i:3 (&rarr PDB)
Source: Information STRUCTURE OF THE RIBOSOMAL 80S-EEF2-SORDARIN COMPLEX FROM YEAST OBTAINED BY DOCKING ATOMIC MODELS FOR RNA AND PROTEIN COMPONENTS INTO A 11.7 A CRYO-EM MAP. THIS FILE, 1S1I, CONTAINS 60S SUBUNIT. THE 40S RIBOSOMAL SUBUNIT IS IN FILE 1S1H.
Source: Compound 5.8S/25S RIBOSOMAL RNAILS: REPRESENTED BY THE ANALOGOUS MOLECULE OF H.
FLIPPED INTERNAL
Source: Resolution 1.70 ANGSTROMS.
Position (1666, 1687), (1671, 1681)
Primary structure ('_': anchors) _AGGAA_-_GGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: O4'-exo, 5: C2'-endo, 8: C2'-endo, 9: C4'-exo, 11: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		8: syn, 9: syn, 11: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 10 →
4 4 11 &larr
5 6 9 ↓
6 6 10 ↑
7 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 13 Watson-Crick/Watson-Crick cis
2 2 12 Bifurcated/O2' trans
3 3 4 Hoogsteen/O2' ?
4 3 11 O2'/Bifurcated trans y
5 3 12 O2'/Bifurcated ?
6 4 10 O2'/Bifurcated trans
7 4 11 O2'/Bifurcated ?
8 7 8 Watson-Crick/Watson-Crick cis
9 7 10 O2'/Watson-Crick trans y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters